Starting phenix.real_space_refine on Mon Apr 6 08:53:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wug_32830/04_2026/7wug_32830.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wug_32830/04_2026/7wug_32830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wug_32830/04_2026/7wug_32830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wug_32830/04_2026/7wug_32830.map" model { file = "/net/cci-nas-00/data/ceres_data/7wug_32830/04_2026/7wug_32830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wug_32830/04_2026/7wug_32830.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 11333 2.51 5 N 2919 2.21 5 O 3171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17515 Number of models: 1 Model: "" Number of chains: 5 Chain: "5" Number of atoms: 6212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6212 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 23, 'TRANS': 758} Chain breaks: 7 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 14, 'GLN:plan1': 5, 'ASP:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "8" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2351 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 10, 'TRANS': 306} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 13, 'ASP:plan': 3, 'HIS:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 6, 'ASN:plan1': 5, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 152 Chain: "1" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3103 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 13, 'TRANS': 388} Chain breaks: 10 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 5, 'GLU:plan': 10, 'HIS:plan': 1, 'TRP:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 101 Chain: "4" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1859 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "Y" Number of atoms: 3990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3990 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 21, 'TRANS': 486} Chain breaks: 9 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 8, 'HIS:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 3, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 83 Time building chain proxies: 3.55, per 1000 atoms: 0.20 Number of scatterers: 17515 At special positions: 0 Unit cell: (165.68, 113.36, 158.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 3171 8.00 N 2919 7.00 C 11333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 756.1 milliseconds 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4306 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 16 sheets defined 50.2% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain '5' and resid 6 through 17 Processing helix chain '5' and resid 21 through 30 Processing helix chain '5' and resid 34 through 41 removed outlier: 3.535A pdb=" N CYS 5 38 " --> pdb=" O GLN 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 62 Processing helix chain '5' and resid 65 through 73 Processing helix chain '5' and resid 73 through 86 removed outlier: 4.194A pdb=" N PHE 5 77 " --> pdb=" O GLY 5 73 " (cutoff:3.500A) Processing helix chain '5' and resid 97 through 115 Processing helix chain '5' and resid 122 through 137 removed outlier: 3.732A pdb=" N LEU 5 126 " --> pdb=" O ASP 5 122 " (cutoff:3.500A) Processing helix chain '5' and resid 144 through 160 removed outlier: 3.528A pdb=" N LEU 5 160 " --> pdb=" O LYS 5 156 " (cutoff:3.500A) Processing helix chain '5' and resid 187 through 205 Processing helix chain '5' and resid 207 through 211 removed outlier: 3.830A pdb=" N GLN 5 210 " --> pdb=" O TYR 5 207 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE 5 211 " --> pdb=" O LEU 5 208 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 207 through 211' Processing helix chain '5' and resid 254 through 272 Processing helix chain '5' and resid 284 through 295 Processing helix chain '5' and resid 299 through 311 Processing helix chain '5' and resid 312 through 317 removed outlier: 3.622A pdb=" N THR 5 316 " --> pdb=" O GLN 5 312 " (cutoff:3.500A) Processing helix chain '5' and resid 323 through 338 removed outlier: 3.913A pdb=" N LEU 5 327 " --> pdb=" O ASP 5 323 " (cutoff:3.500A) Proline residue: 5 332 - end of helix Processing helix chain '5' and resid 348 through 364 Processing helix chain '5' and resid 368 through 376 Processing helix chain '5' and resid 378 through 391 removed outlier: 3.949A pdb=" N CYS 5 382 " --> pdb=" O ASN 5 378 " (cutoff:3.500A) Processing helix chain '5' and resid 397 through 415 removed outlier: 3.517A pdb=" N ALA 5 415 " --> pdb=" O CYS 5 411 " (cutoff:3.500A) Processing helix chain '5' and resid 418 through 427 Processing helix chain '5' and resid 430 through 452 removed outlier: 3.562A pdb=" N HIS 5 434 " --> pdb=" O LEU 5 430 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU 5 452 " --> pdb=" O ASP 5 448 " (cutoff:3.500A) Processing helix chain '5' and resid 452 through 457 removed outlier: 3.581A pdb=" N ILE 5 456 " --> pdb=" O LEU 5 452 " (cutoff:3.500A) Processing helix chain '5' and resid 473 through 489 Processing helix chain '5' and resid 490 through 496 Processing helix chain '5' and resid 500 through 521 removed outlier: 4.131A pdb=" N ALA 5 504 " --> pdb=" O ARG 5 500 " (cutoff:3.500A) Processing helix chain '5' and resid 522 through 524 No H-bonds generated for 'chain '5' and resid 522 through 524' Processing helix chain '5' and resid 525 through 547 removed outlier: 3.538A pdb=" N MET 5 529 " --> pdb=" O GLY 5 525 " (cutoff:3.500A) Proline residue: 5 531 - end of helix Processing helix chain '5' and resid 553 through 560 Processing helix chain '5' and resid 561 through 571 removed outlier: 3.839A pdb=" N ILE 5 565 " --> pdb=" O GLY 5 561 " (cutoff:3.500A) Processing helix chain '5' and resid 585 through 593 Processing helix chain '5' and resid 597 through 612 removed outlier: 3.546A pdb=" N LYS 5 601 " --> pdb=" O VAL 5 597 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET 5 612 " --> pdb=" O LEU 5 608 " (cutoff:3.500A) Processing helix chain '5' and resid 616 through 627 removed outlier: 3.599A pdb=" N LYS 5 620 " --> pdb=" O GLN 5 616 " (cutoff:3.500A) Processing helix chain '5' and resid 628 through 635 removed outlier: 3.956A pdb=" N ILE 5 632 " --> pdb=" O PRO 5 628 " (cutoff:3.500A) Processing helix chain '5' and resid 636 through 638 No H-bonds generated for 'chain '5' and resid 636 through 638' Processing helix chain '5' and resid 640 through 656 Processing helix chain '5' and resid 658 through 669 removed outlier: 3.673A pdb=" N VAL 5 662 " --> pdb=" O SER 5 658 " (cutoff:3.500A) Processing helix chain '5' and resid 690 through 700 Processing helix chain '5' and resid 706 through 724 Processing helix chain '5' and resid 727 through 737 removed outlier: 3.545A pdb=" N LYS 5 731 " --> pdb=" O ASN 5 727 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN 5 737 " --> pdb=" O LEU 5 733 " (cutoff:3.500A) Processing helix chain '5' and resid 738 through 749 Processing helix chain '5' and resid 761 through 776 removed outlier: 3.615A pdb=" N LYS 5 765 " --> pdb=" O ASP 5 761 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU 5 776 " --> pdb=" O LEU 5 772 " (cutoff:3.500A) Processing helix chain '5' and resid 778 through 787 Processing helix chain '5' and resid 869 through 887 Processing helix chain '5' and resid 887 through 897 removed outlier: 4.144A pdb=" N LEU 5 891 " --> pdb=" O GLY 5 887 " (cutoff:3.500A) Processing helix chain '5' and resid 900 through 919 removed outlier: 3.579A pdb=" N LYS 5 919 " --> pdb=" O ASP 5 915 " (cutoff:3.500A) Processing helix chain '8' and resid 35 through 54 Processing helix chain '8' and resid 88 through 100 Processing helix chain '8' and resid 102 through 113 removed outlier: 3.813A pdb=" N SER 8 106 " --> pdb=" O TYR 8 102 " (cutoff:3.500A) Processing helix chain '8' and resid 118 through 130 Processing helix chain '8' and resid 130 through 144 Processing helix chain '8' and resid 145 through 157 Processing helix chain '8' and resid 159 through 164 removed outlier: 3.517A pdb=" N GLU 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '8' and resid 193 through 212 Processing helix chain '8' and resid 220 through 234 removed outlier: 4.014A pdb=" N LEU 8 234 " --> pdb=" O SER 8 230 " (cutoff:3.500A) Processing helix chain '8' and resid 234 through 241 removed outlier: 4.143A pdb=" N SER 8 241 " --> pdb=" O LYS 8 237 " (cutoff:3.500A) Processing helix chain '8' and resid 241 through 256 removed outlier: 3.559A pdb=" N LEU 8 256 " --> pdb=" O MET 8 252 " (cutoff:3.500A) Processing helix chain '8' and resid 280 through 308 removed outlier: 3.844A pdb=" N SER 8 284 " --> pdb=" O ILE 8 280 " (cutoff:3.500A) Proline residue: 8 300 - end of helix Processing helix chain '8' and resid 352 through 357 removed outlier: 3.875A pdb=" N MET 8 357 " --> pdb=" O ASN 8 354 " (cutoff:3.500A) Processing helix chain '8' and resid 394 through 403 removed outlier: 3.506A pdb=" N GLN 8 398 " --> pdb=" O ASN 8 394 " (cutoff:3.500A) Processing helix chain '8' and resid 417 through 422 Processing helix chain '8' and resid 423 through 426 removed outlier: 3.709A pdb=" N GLU 8 426 " --> pdb=" O PHE 8 423 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 423 through 426' Processing helix chain '8' and resid 427 through 446 removed outlier: 3.608A pdb=" N GLN 8 431 " --> pdb=" O PRO 8 427 " (cutoff:3.500A) Processing helix chain '1' and resid 17 through 27 Processing helix chain '1' and resid 30 through 35 removed outlier: 3.520A pdb=" N GLN 1 33 " --> pdb=" O TYR 1 30 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN 1 34 " --> pdb=" O LEU 1 31 " (cutoff:3.500A) Proline residue: 1 35 - end of helix No H-bonds generated for 'chain '1' and resid 30 through 35' Processing helix chain '1' and resid 36 through 47 removed outlier: 3.514A pdb=" N LEU 1 40 " --> pdb=" O VAL 1 36 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS 1 47 " --> pdb=" O LEU 1 43 " (cutoff:3.500A) Processing helix chain '1' and resid 81 through 92 Processing helix chain '1' and resid 117 through 125 Processing helix chain '1' and resid 327 through 332 removed outlier: 3.650A pdb=" N GLY 1 332 " --> pdb=" O TYR 1 328 " (cutoff:3.500A) Processing helix chain '1' and resid 497 through 504 Processing helix chain '1' and resid 596 through 614 removed outlier: 3.686A pdb=" N TYR 1 600 " --> pdb=" O ASP 1 596 " (cutoff:3.500A) Processing helix chain '1' and resid 708 through 725 Processing helix chain '1' and resid 727 through 742 Processing helix chain '1' and resid 752 through 772 Processing helix chain '1' and resid 914 through 932 Processing helix chain '1' and resid 944 through 949 removed outlier: 3.652A pdb=" N ILE 1 949 " --> pdb=" O TYR 1 946 " (cutoff:3.500A) Processing helix chain '1' and resid 950 through 955 Processing helix chain '4' and resid 92 through 97 Processing helix chain '4' and resid 212 through 222 Processing helix chain '4' and resid 223 through 232 removed outlier: 3.686A pdb=" N ARG 4 227 " --> pdb=" O PHE 4 223 " (cutoff:3.500A) Processing helix chain '4' and resid 270 through 277 Processing helix chain '4' and resid 281 through 285 removed outlier: 3.627A pdb=" N GLU 4 285 " --> pdb=" O TYR 4 282 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 102 Processing helix chain 'Y' and resid 186 through 196 Processing helix chain 'Y' and resid 280 through 297 removed outlier: 3.712A pdb=" N VAL Y 284 " --> pdb=" O PRO Y 280 " (cutoff:3.500A) Processing helix chain 'Y' and resid 307 through 315 removed outlier: 3.644A pdb=" N VAL Y 311 " --> pdb=" O SER Y 307 " (cutoff:3.500A) Processing helix chain 'Y' and resid 319 through 328 Processing helix chain 'Y' and resid 336 through 346 Processing helix chain 'Y' and resid 543 through 553 Processing helix chain 'Y' and resid 589 through 593 removed outlier: 3.779A pdb=" N ARG Y 592 " --> pdb=" O ASN Y 589 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN Y 593 " --> pdb=" O LEU Y 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 589 through 593' Processing sheet with id=AA1, first strand: chain '5' and resid 216 through 217 removed outlier: 3.844A pdb=" N VAL 5 217 " --> pdb=" O VAL 1 110 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL 1 110 " --> pdb=" O VAL 5 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '8' and resid 32 through 33 removed outlier: 6.613A pdb=" N LYS 8 32 " --> pdb=" O GLY 8 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '8' and resid 330 through 331 removed outlier: 3.936A pdb=" N PHE 8 415 " --> pdb=" O TYR 8 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 347 through 349 Processing sheet with id=AA5, first strand: chain '1' and resid 396 through 399 removed outlier: 3.573A pdb=" N LEU 1 518 " --> pdb=" O CYS 1 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 557 through 563 removed outlier: 5.591A pdb=" N HIS 1 558 " --> pdb=" O LYS 1 554 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS 1 554 " --> pdb=" O HIS 1 558 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY 1 560 " --> pdb=" O PHE 1 552 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE 1 552 " --> pdb=" O GLY 1 560 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE 1 550 " --> pdb=" O ALA 1 562 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER 1 582 " --> pdb=" O LEU 1 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 687 through 688 Processing sheet with id=AA8, first strand: chain '4' and resid 340 through 341 removed outlier: 4.131A pdb=" N GLN 4 340 " --> pdb=" O TYR 4 331 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER 4 164 " --> pdb=" O LYS 4 147 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N SER 4 180 " --> pdb=" O LEU 4 297 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU 4 297 " --> pdb=" O SER 4 180 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR 4 182 " --> pdb=" O LYS 4 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 32 through 35 removed outlier: 6.308A pdb=" N ALA Y 9 " --> pdb=" O LEU Y 677 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU Y 677 " --> pdb=" O ALA Y 9 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER Y 11 " --> pdb=" O LEU Y 675 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU Y 675 " --> pdb=" O SER Y 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 158 through 161 removed outlier: 4.724A pdb=" N TYR Y 56 " --> pdb=" O TYR Y 161 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU Y 212 " --> pdb=" O ARG Y 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Y' and resid 128 through 134 Processing sheet with id=AB3, first strand: chain 'Y' and resid 164 through 165 removed outlier: 6.947A pdb=" N TYR Y 165 " --> pdb=" O ILE Y 615 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ASP Y 617 " --> pdb=" O TYR Y 165 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL Y 613 " --> pdb=" O VAL Y 633 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL Y 633 " --> pdb=" O VAL Y 613 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE Y 615 " --> pdb=" O HIS Y 631 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS Y 631 " --> pdb=" O ILE Y 615 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR Y 635 " --> pdb=" O ASN Y 609 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 164 through 165 removed outlier: 6.947A pdb=" N TYR Y 165 " --> pdb=" O ILE Y 615 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ASP Y 617 " --> pdb=" O TYR Y 165 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL Y 613 " --> pdb=" O VAL Y 633 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL Y 633 " --> pdb=" O VAL Y 613 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE Y 615 " --> pdb=" O HIS Y 631 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS Y 631 " --> pdb=" O ILE Y 615 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU Y 640 " --> pdb=" O SER Y 636 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LYS Y 645 " --> pdb=" O LEU Y 659 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU Y 659 " --> pdb=" O LYS Y 645 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU Y 647 " --> pdb=" O ILE Y 657 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE Y 657 " --> pdb=" O GLU Y 647 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 252 through 255 removed outlier: 6.557A pdb=" N ILE Y 274 " --> pdb=" O VAL Y 357 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 441 through 448 Processing sheet with id=AB7, first strand: chain 'Y' and resid 559 through 561 915 hydrogen bonds defined for protein. 2652 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5544 1.34 - 1.46: 4217 1.46 - 1.58: 7976 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 17873 Sorted by residual: bond pdb=" C GLN 5 312 " pdb=" N PRO 5 313 " ideal model delta sigma weight residual 1.335 1.378 -0.044 1.19e-02 7.06e+03 1.35e+01 bond pdb=" N ILE Y 570 " pdb=" CA ILE Y 570 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.21e-02 6.83e+03 9.29e+00 bond pdb=" N ASP Y 572 " pdb=" CA ASP Y 572 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.38e+00 bond pdb=" N GLY Y 575 " pdb=" CA GLY Y 575 " ideal model delta sigma weight residual 1.449 1.475 -0.026 9.80e-03 1.04e+04 6.80e+00 bond pdb=" N LYS 1 408 " pdb=" CA LYS 1 408 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.14e-02 7.69e+03 5.94e+00 ... (remaining 17868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 23819 2.26 - 4.52: 341 4.52 - 6.78: 55 6.78 - 9.04: 11 9.04 - 11.30: 1 Bond angle restraints: 24227 Sorted by residual: angle pdb=" N GLY Y 575 " pdb=" CA GLY Y 575 " pdb=" C GLY Y 575 " ideal model delta sigma weight residual 110.56 117.83 -7.27 1.36e+00 5.41e-01 2.86e+01 angle pdb=" N THR Y 573 " pdb=" CA THR Y 573 " pdb=" C THR Y 573 " ideal model delta sigma weight residual 113.38 107.41 5.97 1.23e+00 6.61e-01 2.36e+01 angle pdb=" C PHE Y 492 " pdb=" N VAL Y 493 " pdb=" CA VAL Y 493 " ideal model delta sigma weight residual 121.97 129.10 -7.13 1.80e+00 3.09e-01 1.57e+01 angle pdb=" C PHE 1 595 " pdb=" N ASP 1 596 " pdb=" CA ASP 1 596 " ideal model delta sigma weight residual 121.54 128.79 -7.25 1.91e+00 2.74e-01 1.44e+01 angle pdb=" CA VAL 5 547 " pdb=" CB VAL 5 547 " pdb=" CG1 VAL 5 547 " ideal model delta sigma weight residual 110.40 116.82 -6.42 1.70e+00 3.46e-01 1.43e+01 ... (remaining 24222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 9653 17.49 - 34.99: 842 34.99 - 52.48: 127 52.48 - 69.98: 17 69.98 - 87.47: 11 Dihedral angle restraints: 10650 sinusoidal: 4040 harmonic: 6610 Sorted by residual: dihedral pdb=" CA TYR 5 271 " pdb=" C TYR 5 271 " pdb=" N HIS 5 272 " pdb=" CA HIS 5 272 " ideal model delta harmonic sigma weight residual 180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ASP Y 610 " pdb=" C ASP Y 610 " pdb=" N THR Y 611 " pdb=" CA THR Y 611 " ideal model delta harmonic sigma weight residual -180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PHE 1 595 " pdb=" C PHE 1 595 " pdb=" N ASP 1 596 " pdb=" CA ASP 1 596 " ideal model delta harmonic sigma weight residual -180.00 -156.13 -23.87 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 10647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1854 0.038 - 0.077: 690 0.077 - 0.115: 182 0.115 - 0.153: 58 0.153 - 0.192: 11 Chirality restraints: 2795 Sorted by residual: chirality pdb=" CB VAL 4 345 " pdb=" CA VAL 4 345 " pdb=" CG1 VAL 4 345 " pdb=" CG2 VAL 4 345 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CB VAL 5 749 " pdb=" CA VAL 5 749 " pdb=" CG1 VAL 5 749 " pdb=" CG2 VAL 5 749 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA ILE Y 570 " pdb=" N ILE Y 570 " pdb=" C ILE Y 570 " pdb=" CB ILE Y 570 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 2792 not shown) Planarity restraints: 3049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL 4 345 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO 4 346 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO 4 346 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO 4 346 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG 4 124 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO 4 125 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO 4 125 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO 4 125 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN 1 34 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO 1 35 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO 1 35 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO 1 35 " 0.027 5.00e-02 4.00e+02 ... (remaining 3046 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2813 2.76 - 3.30: 15372 3.30 - 3.83: 27672 3.83 - 4.37: 32080 4.37 - 4.90: 58796 Nonbonded interactions: 136733 Sorted by model distance: nonbonded pdb=" O GLY Y 249 " pdb=" OG SER Y 267 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR 4 117 " pdb=" OD1 ASP 4 150 " model vdw 2.260 3.040 nonbonded pdb=" OD2 ASP 4 321 " pdb=" OG1 THR 4 324 " model vdw 2.262 3.040 nonbonded pdb=" O ILE Y 73 " pdb=" OH TYR Y 198 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR 5 889 " pdb=" OD1 ASP 5 915 " model vdw 2.287 3.040 ... (remaining 136728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.960 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17873 Z= 0.180 Angle : 0.690 11.304 24227 Z= 0.379 Chirality : 0.045 0.192 2795 Planarity : 0.005 0.056 3049 Dihedral : 13.453 87.475 6344 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.12 % Favored : 95.84 % Rotamer: Outliers : 0.11 % Allowed : 0.43 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2161 helix: 0.45 (0.15), residues: 1013 sheet: 0.38 (0.31), residues: 300 loop : -1.56 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 4 124 TYR 0.020 0.002 TYR Y 56 PHE 0.021 0.002 PHE 8 195 TRP 0.012 0.001 TRP 5 770 HIS 0.005 0.001 HIS 5 272 Details of bonding type rmsd covalent geometry : bond 0.00365 (17873) covalent geometry : angle 0.69000 (24227) hydrogen bonds : bond 0.13613 ( 909) hydrogen bonds : angle 5.60262 ( 2652) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: 5 761 ASP cc_start: 0.7733 (t0) cc_final: 0.7495 (t0) REVERT: 1 720 ASP cc_start: 0.8093 (m-30) cc_final: 0.7712 (m-30) REVERT: 4 93 LYS cc_start: 0.8969 (ttmt) cc_final: 0.8622 (ttpt) REVERT: 4 115 ASN cc_start: 0.8030 (m110) cc_final: 0.7726 (m110) REVERT: Y 573 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8827 (p) outliers start: 2 outliers final: 1 residues processed: 191 average time/residue: 0.1297 time to fit residues: 38.6892 Evaluate side-chains 157 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 571 LEU Chi-restraints excluded: chain Y residue 573 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 9 ASN ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 334 ASN 8 337 ASN 4 275 GLN Y 15 ASN Y 360 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.097825 restraints weight = 25983.254| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.80 r_work: 0.2907 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17873 Z= 0.116 Angle : 0.500 6.927 24227 Z= 0.264 Chirality : 0.040 0.148 2795 Planarity : 0.003 0.046 3049 Dihedral : 4.258 38.749 2386 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 0.65 % Allowed : 5.03 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 2161 helix: 1.60 (0.16), residues: 1031 sheet: 0.56 (0.31), residues: 292 loop : -1.39 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 694 TYR 0.016 0.001 TYR Y 56 PHE 0.014 0.001 PHE Y 54 TRP 0.010 0.001 TRP 8 39 HIS 0.005 0.000 HIS 5 272 Details of bonding type rmsd covalent geometry : bond 0.00268 (17873) covalent geometry : angle 0.50014 (24227) hydrogen bonds : bond 0.04371 ( 909) hydrogen bonds : angle 4.23250 ( 2652) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: 5 257 ASP cc_start: 0.8710 (m-30) cc_final: 0.8443 (m-30) REVERT: 8 351 GLN cc_start: 0.8922 (tt0) cc_final: 0.8674 (tt0) REVERT: 1 720 ASP cc_start: 0.8487 (m-30) cc_final: 0.8119 (m-30) REVERT: 4 93 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8201 (ttpt) REVERT: 4 98 ASP cc_start: 0.8803 (t0) cc_final: 0.8576 (t0) REVERT: 4 115 ASN cc_start: 0.8069 (m110) cc_final: 0.7722 (m110) REVERT: 4 300 ASP cc_start: 0.8174 (m-30) cc_final: 0.7880 (m-30) REVERT: Y 168 MET cc_start: 0.7977 (ptp) cc_final: 0.7749 (ptt) REVERT: Y 668 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8296 (mtmt) outliers start: 12 outliers final: 7 residues processed: 186 average time/residue: 0.1322 time to fit residues: 38.3931 Evaluate side-chains 170 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 255 MET Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 8 residue 159 LEU Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain Y residue 571 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 95 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 176 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 301 ASN 8 337 ASN Y 631 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.097220 restraints weight = 26186.880| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.84 r_work: 0.2897 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17873 Z= 0.118 Angle : 0.483 6.410 24227 Z= 0.254 Chirality : 0.040 0.143 2795 Planarity : 0.003 0.044 3049 Dihedral : 4.006 34.574 2385 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 0.65 % Allowed : 6.81 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.19), residues: 2161 helix: 2.01 (0.16), residues: 1035 sheet: 0.54 (0.31), residues: 292 loop : -1.28 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 4 124 TYR 0.017 0.001 TYR 5 273 PHE 0.013 0.001 PHE Y 54 TRP 0.009 0.001 TRP 8 39 HIS 0.006 0.001 HIS 5 272 Details of bonding type rmsd covalent geometry : bond 0.00278 (17873) covalent geometry : angle 0.48304 (24227) hydrogen bonds : bond 0.04194 ( 909) hydrogen bonds : angle 4.04039 ( 2652) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.741 Fit side-chains REVERT: 5 257 ASP cc_start: 0.8740 (m-30) cc_final: 0.8478 (m-30) REVERT: 8 351 GLN cc_start: 0.8932 (tt0) cc_final: 0.8706 (tt0) REVERT: 1 24 ASN cc_start: 0.8641 (m110) cc_final: 0.8310 (m-40) REVERT: 1 720 ASP cc_start: 0.8520 (m-30) cc_final: 0.8138 (m-30) REVERT: 4 93 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8282 (ttpt) REVERT: 4 115 ASN cc_start: 0.8115 (m110) cc_final: 0.7739 (m110) REVERT: 4 300 ASP cc_start: 0.8135 (m-30) cc_final: 0.7753 (m-30) REVERT: Y 168 MET cc_start: 0.8013 (ptp) cc_final: 0.7718 (ptt) REVERT: Y 668 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8324 (mtmt) outliers start: 12 outliers final: 8 residues processed: 180 average time/residue: 0.1292 time to fit residues: 36.5548 Evaluate side-chains 172 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 599 GLU Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain Y residue 264 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 167 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 192 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 126 optimal weight: 0.0170 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN Y 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.092911 restraints weight = 26299.054| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.81 r_work: 0.2824 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17873 Z= 0.210 Angle : 0.570 8.603 24227 Z= 0.298 Chirality : 0.042 0.164 2795 Planarity : 0.004 0.045 3049 Dihedral : 4.183 23.441 2383 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.66 % Favored : 96.30 % Rotamer: Outliers : 1.19 % Allowed : 8.55 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.18), residues: 2161 helix: 1.95 (0.16), residues: 1034 sheet: 0.41 (0.30), residues: 292 loop : -1.33 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 4 124 TYR 0.020 0.002 TYR 5 333 PHE 0.015 0.002 PHE 8 195 TRP 0.010 0.001 TRP 8 39 HIS 0.005 0.001 HIS 5 272 Details of bonding type rmsd covalent geometry : bond 0.00521 (17873) covalent geometry : angle 0.56974 (24227) hydrogen bonds : bond 0.05509 ( 909) hydrogen bonds : angle 4.17296 ( 2652) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.717 Fit side-chains REVERT: 8 351 GLN cc_start: 0.8968 (tt0) cc_final: 0.8677 (tt0) REVERT: 1 24 ASN cc_start: 0.8629 (m110) cc_final: 0.8310 (m-40) REVERT: 1 111 TYR cc_start: 0.8163 (m-10) cc_final: 0.7935 (m-10) REVERT: 1 536 ASP cc_start: 0.8498 (t0) cc_final: 0.8165 (t0) REVERT: 1 720 ASP cc_start: 0.8614 (m-30) cc_final: 0.8161 (m-30) REVERT: 4 93 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8365 (ttpt) REVERT: 4 115 ASN cc_start: 0.8126 (m110) cc_final: 0.7786 (m110) REVERT: 4 300 ASP cc_start: 0.8087 (m-30) cc_final: 0.7659 (m-30) REVERT: Y 168 MET cc_start: 0.8041 (ptp) cc_final: 0.7819 (ptt) REVERT: Y 336 ASN cc_start: 0.8297 (t0) cc_final: 0.7725 (t0) outliers start: 22 outliers final: 13 residues processed: 178 average time/residue: 0.1257 time to fit residues: 35.6584 Evaluate side-chains 172 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 467 CYS Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 1 residue 592 ASP Chi-restraints excluded: chain 1 residue 706 ASP Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 264 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 202 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.096150 restraints weight = 26016.451| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.82 r_work: 0.2885 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17873 Z= 0.114 Angle : 0.486 13.583 24227 Z= 0.255 Chirality : 0.040 0.140 2795 Planarity : 0.003 0.043 3049 Dihedral : 3.953 23.878 2383 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % Rotamer: Outliers : 1.03 % Allowed : 9.95 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 2161 helix: 2.21 (0.16), residues: 1035 sheet: 0.51 (0.30), residues: 291 loop : -1.24 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG 5 652 TYR 0.018 0.001 TYR 5 273 PHE 0.016 0.001 PHE 8 195 TRP 0.009 0.001 TRP 8 39 HIS 0.007 0.000 HIS 5 272 Details of bonding type rmsd covalent geometry : bond 0.00267 (17873) covalent geometry : angle 0.48628 (24227) hydrogen bonds : bond 0.04063 ( 909) hydrogen bonds : angle 3.99483 ( 2652) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.683 Fit side-chains REVERT: 8 351 GLN cc_start: 0.8960 (tt0) cc_final: 0.8732 (tt0) REVERT: 1 24 ASN cc_start: 0.8631 (m110) cc_final: 0.8409 (m-40) REVERT: 1 720 ASP cc_start: 0.8544 (m-30) cc_final: 0.8142 (m-30) REVERT: 4 93 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8301 (ttpt) REVERT: 4 115 ASN cc_start: 0.8132 (m110) cc_final: 0.7784 (m110) REVERT: 4 300 ASP cc_start: 0.8078 (m-30) cc_final: 0.7581 (m-30) REVERT: Y 168 MET cc_start: 0.8011 (ptp) cc_final: 0.7784 (ptt) REVERT: Y 264 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8868 (mtm) REVERT: Y 336 ASN cc_start: 0.8206 (t0) cc_final: 0.7667 (t0) REVERT: Y 668 LYS cc_start: 0.8687 (mmmt) cc_final: 0.8276 (mtmt) outliers start: 19 outliers final: 12 residues processed: 183 average time/residue: 0.1306 time to fit residues: 37.3754 Evaluate side-chains 177 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 255 MET Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 467 CYS Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 544 CYS Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 1 residue 706 ASP Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 264 MET Chi-restraints excluded: chain Y residue 306 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 198 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 194 optimal weight: 0.2980 chunk 95 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 208 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN 1 957 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.095564 restraints weight = 26109.298| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.86 r_work: 0.2867 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17873 Z= 0.124 Angle : 0.487 6.813 24227 Z= 0.257 Chirality : 0.040 0.141 2795 Planarity : 0.003 0.040 3049 Dihedral : 3.889 23.730 2383 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.34 % Rotamer: Outliers : 1.19 % Allowed : 10.76 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.19), residues: 2161 helix: 2.30 (0.16), residues: 1036 sheet: 0.54 (0.30), residues: 291 loop : -1.24 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 4 124 TYR 0.020 0.001 TYR 5 333 PHE 0.016 0.001 PHE 8 195 TRP 0.008 0.001 TRP 8 39 HIS 0.006 0.001 HIS 5 272 Details of bonding type rmsd covalent geometry : bond 0.00294 (17873) covalent geometry : angle 0.48697 (24227) hydrogen bonds : bond 0.04197 ( 909) hydrogen bonds : angle 3.93172 ( 2652) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.698 Fit side-chains REVERT: 5 257 ASP cc_start: 0.8827 (m-30) cc_final: 0.8510 (m-30) REVERT: 8 351 GLN cc_start: 0.8950 (tt0) cc_final: 0.8699 (tt0) REVERT: 1 24 ASN cc_start: 0.8629 (m110) cc_final: 0.8299 (m-40) REVERT: 1 720 ASP cc_start: 0.8569 (m-30) cc_final: 0.8165 (m-30) REVERT: 4 93 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8289 (ttpt) REVERT: 4 115 ASN cc_start: 0.8140 (m110) cc_final: 0.7794 (m110) REVERT: 4 150 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: 4 300 ASP cc_start: 0.8043 (m-30) cc_final: 0.7560 (m-30) REVERT: Y 168 MET cc_start: 0.8078 (ptp) cc_final: 0.7811 (ptt) REVERT: Y 172 CYS cc_start: 0.8214 (p) cc_final: 0.7902 (p) REVERT: Y 264 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8920 (mtm) REVERT: Y 336 ASN cc_start: 0.8165 (t0) cc_final: 0.7610 (t0) REVERT: Y 668 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8313 (mtmt) outliers start: 22 outliers final: 16 residues processed: 185 average time/residue: 0.1285 time to fit residues: 37.5984 Evaluate side-chains 184 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 255 MET Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 467 CYS Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 544 CYS Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 1 residue 706 ASP Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 150 ASP Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 4 residue 345 VAL Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 207 ILE Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 264 MET Chi-restraints excluded: chain Y residue 306 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 53 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 185 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN 1 957 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.095934 restraints weight = 26070.946| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.83 r_work: 0.2863 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17873 Z= 0.119 Angle : 0.483 7.923 24227 Z= 0.254 Chirality : 0.040 0.145 2795 Planarity : 0.003 0.041 3049 Dihedral : 3.852 23.955 2383 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.42 % Favored : 96.53 % Rotamer: Outliers : 1.46 % Allowed : 11.14 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.19), residues: 2161 helix: 2.28 (0.16), residues: 1049 sheet: 0.49 (0.30), residues: 297 loop : -1.26 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 4 124 TYR 0.019 0.001 TYR 5 333 PHE 0.016 0.001 PHE 8 195 TRP 0.008 0.001 TRP 8 39 HIS 0.006 0.001 HIS 5 272 Details of bonding type rmsd covalent geometry : bond 0.00280 (17873) covalent geometry : angle 0.48267 (24227) hydrogen bonds : bond 0.04080 ( 909) hydrogen bonds : angle 3.90829 ( 2652) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.537 Fit side-chains REVERT: 5 257 ASP cc_start: 0.8802 (m-30) cc_final: 0.8504 (m-30) REVERT: 8 351 GLN cc_start: 0.8946 (tt0) cc_final: 0.8696 (tt0) REVERT: 1 24 ASN cc_start: 0.8605 (m110) cc_final: 0.8261 (m-40) REVERT: 1 720 ASP cc_start: 0.8527 (m-30) cc_final: 0.8113 (m-30) REVERT: 4 93 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8259 (ttpt) REVERT: 4 115 ASN cc_start: 0.8127 (m110) cc_final: 0.7752 (m110) REVERT: 4 150 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: 4 300 ASP cc_start: 0.8020 (m-30) cc_final: 0.7516 (m-30) REVERT: Y 168 MET cc_start: 0.8066 (ptp) cc_final: 0.7787 (ptt) REVERT: Y 172 CYS cc_start: 0.8326 (p) cc_final: 0.8018 (p) REVERT: Y 264 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8936 (mtm) REVERT: Y 336 ASN cc_start: 0.8149 (t0) cc_final: 0.7590 (t0) REVERT: Y 668 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8299 (mtmt) outliers start: 27 outliers final: 15 residues processed: 193 average time/residue: 0.1251 time to fit residues: 38.3347 Evaluate side-chains 186 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 467 CYS Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 544 CYS Chi-restraints excluded: chain 5 residue 599 GLU Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 1 residue 706 ASP Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 150 ASP Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 4 residue 345 VAL Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 207 ILE Chi-restraints excluded: chain Y residue 264 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 150 optimal weight: 0.0970 chunk 61 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 211 optimal weight: 0.0980 chunk 62 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 169 optimal weight: 0.0980 chunk 186 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.098104 restraints weight = 26017.282| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.82 r_work: 0.2900 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17873 Z= 0.092 Angle : 0.465 13.602 24227 Z= 0.243 Chirality : 0.039 0.136 2795 Planarity : 0.003 0.038 3049 Dihedral : 3.701 24.099 2383 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 1.03 % Allowed : 11.79 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.19), residues: 2161 helix: 2.41 (0.16), residues: 1050 sheet: 0.59 (0.31), residues: 292 loop : -1.20 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 4 124 TYR 0.017 0.001 TYR 5 333 PHE 0.013 0.001 PHE Y 498 TRP 0.007 0.001 TRP 8 39 HIS 0.007 0.000 HIS 5 272 Details of bonding type rmsd covalent geometry : bond 0.00202 (17873) covalent geometry : angle 0.46493 (24227) hydrogen bonds : bond 0.03476 ( 909) hydrogen bonds : angle 3.81885 ( 2652) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.637 Fit side-chains REVERT: 5 257 ASP cc_start: 0.8742 (m-30) cc_final: 0.8485 (m-30) REVERT: 8 351 GLN cc_start: 0.8950 (tt0) cc_final: 0.8745 (tt0) REVERT: 1 24 ASN cc_start: 0.8644 (m110) cc_final: 0.8337 (m-40) REVERT: 1 720 ASP cc_start: 0.8579 (m-30) cc_final: 0.8211 (m-30) REVERT: 4 93 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8308 (ttpt) REVERT: 4 115 ASN cc_start: 0.8263 (m110) cc_final: 0.7894 (m110) REVERT: 4 150 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: 4 300 ASP cc_start: 0.8106 (m-30) cc_final: 0.7664 (m-30) REVERT: Y 172 CYS cc_start: 0.8283 (p) cc_final: 0.8001 (p) REVERT: Y 264 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8945 (mtm) REVERT: Y 336 ASN cc_start: 0.8179 (t0) cc_final: 0.7643 (t0) REVERT: Y 668 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8335 (mtmt) outliers start: 19 outliers final: 14 residues processed: 191 average time/residue: 0.1204 time to fit residues: 36.6204 Evaluate side-chains 187 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 255 MET Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 467 CYS Chi-restraints excluded: chain 5 residue 544 CYS Chi-restraints excluded: chain 5 residue 599 GLU Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 1 residue 687 PHE Chi-restraints excluded: chain 4 residue 150 ASP Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 345 VAL Chi-restraints excluded: chain Y residue 207 ILE Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 264 MET Chi-restraints excluded: chain Y residue 306 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 33 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN 1 957 ASN 4 322 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.093619 restraints weight = 26227.410| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.82 r_work: 0.2843 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17873 Z= 0.175 Angle : 0.545 11.892 24227 Z= 0.283 Chirality : 0.041 0.154 2795 Planarity : 0.003 0.041 3049 Dihedral : 3.953 23.991 2383 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.75 % Favored : 96.21 % Rotamer: Outliers : 1.19 % Allowed : 11.84 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.19), residues: 2161 helix: 2.26 (0.16), residues: 1043 sheet: 0.56 (0.30), residues: 292 loop : -1.20 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 4 124 TYR 0.024 0.002 TYR 5 333 PHE 0.015 0.001 PHE 8 195 TRP 0.010 0.001 TRP 4 292 HIS 0.005 0.001 HIS 5 272 Details of bonding type rmsd covalent geometry : bond 0.00429 (17873) covalent geometry : angle 0.54497 (24227) hydrogen bonds : bond 0.04891 ( 909) hydrogen bonds : angle 3.99189 ( 2652) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.738 Fit side-chains REVERT: 5 728 GLU cc_start: 0.8334 (mp0) cc_final: 0.7991 (mp0) REVERT: 8 351 GLN cc_start: 0.8981 (tt0) cc_final: 0.8713 (tt0) REVERT: 1 24 ASN cc_start: 0.8742 (m110) cc_final: 0.8442 (m-40) REVERT: 1 536 ASP cc_start: 0.8413 (t0) cc_final: 0.8155 (t0) REVERT: 1 720 ASP cc_start: 0.8592 (m-30) cc_final: 0.8171 (m-30) REVERT: 4 93 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8321 (ttpt) REVERT: 4 115 ASN cc_start: 0.8148 (m110) cc_final: 0.7794 (m110) REVERT: 4 150 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: 4 300 ASP cc_start: 0.8056 (m-30) cc_final: 0.7579 (m-30) REVERT: Y 168 MET cc_start: 0.8113 (ptp) cc_final: 0.7833 (ptt) REVERT: Y 172 CYS cc_start: 0.8320 (p) cc_final: 0.8021 (p) REVERT: Y 264 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8929 (mtm) REVERT: Y 336 ASN cc_start: 0.8177 (t0) cc_final: 0.7625 (t0) outliers start: 22 outliers final: 14 residues processed: 178 average time/residue: 0.1216 time to fit residues: 34.5874 Evaluate side-chains 178 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 467 CYS Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 1 residue 592 ASP Chi-restraints excluded: chain 1 residue 706 ASP Chi-restraints excluded: chain 4 residue 150 ASP Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 221 ILE Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 4 residue 345 VAL Chi-restraints excluded: chain Y residue 207 ILE Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 264 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 165 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 191 optimal weight: 0.0770 chunk 71 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.095306 restraints weight = 25814.868| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.81 r_work: 0.2867 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17873 Z= 0.126 Angle : 0.507 11.275 24227 Z= 0.264 Chirality : 0.040 0.147 2795 Planarity : 0.003 0.042 3049 Dihedral : 3.880 24.589 2383 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 1.08 % Allowed : 12.06 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 2161 helix: 2.32 (0.16), residues: 1042 sheet: 0.57 (0.30), residues: 292 loop : -1.17 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 4 124 TYR 0.020 0.001 TYR 5 333 PHE 0.015 0.001 PHE 8 195 TRP 0.009 0.001 TRP 8 39 HIS 0.006 0.001 HIS 5 272 Details of bonding type rmsd covalent geometry : bond 0.00302 (17873) covalent geometry : angle 0.50708 (24227) hydrogen bonds : bond 0.04191 ( 909) hydrogen bonds : angle 3.93848 ( 2652) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.754 Fit side-chains REVERT: 5 728 GLU cc_start: 0.8321 (mp0) cc_final: 0.7985 (mp0) REVERT: 8 351 GLN cc_start: 0.8974 (tt0) cc_final: 0.8718 (tt0) REVERT: 1 24 ASN cc_start: 0.8719 (m110) cc_final: 0.8378 (m-40) REVERT: 1 720 ASP cc_start: 0.8570 (m-30) cc_final: 0.8144 (m-30) REVERT: 4 93 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8337 (ttpt) REVERT: 4 115 ASN cc_start: 0.8151 (m110) cc_final: 0.7778 (m110) REVERT: 4 300 ASP cc_start: 0.8027 (m-30) cc_final: 0.7521 (m-30) REVERT: Y 168 MET cc_start: 0.8077 (ptp) cc_final: 0.7820 (ptt) REVERT: Y 172 CYS cc_start: 0.8341 (p) cc_final: 0.8048 (p) REVERT: Y 264 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8929 (mtm) REVERT: Y 336 ASN cc_start: 0.8132 (t0) cc_final: 0.7565 (t0) outliers start: 20 outliers final: 14 residues processed: 181 average time/residue: 0.1268 time to fit residues: 36.3336 Evaluate side-chains 183 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 467 CYS Chi-restraints excluded: chain 5 residue 518 THR Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 1 residue 592 ASP Chi-restraints excluded: chain 1 residue 706 ASP Chi-restraints excluded: chain 4 residue 150 ASP Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 4 residue 345 VAL Chi-restraints excluded: chain Y residue 207 ILE Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 264 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 118 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 202 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN 1 957 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.095119 restraints weight = 26184.874| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.84 r_work: 0.2868 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17873 Z= 0.136 Angle : 0.514 10.324 24227 Z= 0.268 Chirality : 0.040 0.149 2795 Planarity : 0.003 0.041 3049 Dihedral : 3.896 24.748 2383 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.34 % Rotamer: Outliers : 0.92 % Allowed : 12.39 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 2161 helix: 2.30 (0.16), residues: 1042 sheet: 0.56 (0.30), residues: 292 loop : -1.17 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 4 124 TYR 0.021 0.001 TYR 5 333 PHE 0.015 0.001 PHE 8 195 TRP 0.008 0.001 TRP 8 39 HIS 0.006 0.001 HIS 5 272 Details of bonding type rmsd covalent geometry : bond 0.00327 (17873) covalent geometry : angle 0.51393 (24227) hydrogen bonds : bond 0.04338 ( 909) hydrogen bonds : angle 3.95370 ( 2652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4194.10 seconds wall clock time: 72 minutes 35.08 seconds (4355.08 seconds total)